debian/changelog

+phyx (1.01+ds-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Removed obsolete 2to3 patch
+  * Adjusted cleanup after build
+  * Not having upstream's auto-generated src/configure in source tree
+
+ -- Steffen Moeller <moeller@debian.org>  Thu, 12 Dec 2019 12:50:28 +0100
+
 phyx (1.0+ds-1) unstable; urgency=medium
 
   * Team upload

debian/control

@@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 12),
                libnlopt-dev,
                libatlas-cpp-0.6-dev,
                libarmadillo-dev
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/phyx
 Vcs-Git: https://salsa.debian.org/med-team/phyx.git
 Homepage: https://github.com/FePhyFoFum/phyx

debian/copyright

@@ -3,6 +3,7 @@ Upstream-Name: phyx
 Source: https://github.com/FePhyFoFum/phyx/releases
 Files-Excluded:
 	deps
+	src/configure
 
 Files: *
 Copyright: 2014-2017 Joseph W. Brown, Joseph F. Walker, and Stephen A. Smith

debian/manpages

-debian/mans/*.1
+#debian/mans/*.1

debian/patches/2to3.patch

-Description: port from python2 to python3
-Author: Shayan Doust <hello@shayandoust.me>
-Bug-Debian: https://bugs.debian.org/937285
-Last-Update: 2019-09-11
----
-
-Index: phyx/src/Phyx_Gui.py
-===================================================================
---- phyx.orig/src/Phyx_Gui.py	2019-09-13 02:52:54.301623771 +0100
-+++ phyx/src/Phyx_Gui.py	2019-09-13 02:52:54.285623836 +0100
-@@ -1,5 +1,5 @@
--import Tkinter,os,sys
--from Tkinter import *
-+import tkinter,os,sys
-+from tkinter import *
- 
- 
- class GUI:
-@@ -12,7 +12,7 @@
- 		#self.label.pack()
- 		
- 		global a
--		a = Tkinter.StringVar()
-+		a = tkinter.StringVar()
- 		self.a_seq = Entry(master, bd=5, textvariable=a).grid(row=0,column=1)
- 		#self.aa_seq.pack(side = LEFT)
- 
-@@ -20,7 +20,7 @@
- 		#self.label.pack(side = LEFT)
- 
- 		global b
--		b = Tkinter.StringVar()
-+		b = tkinter.StringVar()
- 		self.b_seq = Entry(master, bd=5, textvariable=b).grid(row=0,column=3)
- 		#self.b_seq.pack(side = LEFT)
- 		
-@@ -28,7 +28,7 @@
- 		#self.label.pack(side = LEFT)
- 		
- 		global c
--		c = Tkinter.StringVar()
-+		c = tkinter.StringVar()
- 		self.c_seq = Entry(master, bd=5, textvariable=c).grid(row=0,column=5)
- 		#self.c_seq.pack(side = LEFT)
- 		
-@@ -36,118 +36,118 @@
- 		#self.label.pack(side = LEFT)
- 		
- 		global d
--		d = Tkinter.StringVar()
-+		d = tkinter.StringVar()
- 		self.d_seq = Entry(master, bd=5, textvariable=d).grid(row=0,column=7)
- 		#self.d_seq.pack(side = LEFT)
- 		
- 		self.label = Label(master, text="Path to -e").grid(row=1,column=0)		
- 		global e
--		e = Tkinter.StringVar()
-+		e = tkinter.StringVar()
- 		self.e_seq = Entry(master, bd=5, textvariable=e).grid(row=1,column=1)
- 		
- 		self.label = Label(master, text="Path to -f").grid(row=1,column=2)		
- 		global f
--		f = Tkinter.StringVar()
-+		f = tkinter.StringVar()
- 		self.f_seq = Entry(master, bd=5, textvariable=f).grid(row=1,column=3)
- 		
- 		self.label = Label(master, text="Path to -g").grid(row=1,column=4)		
- 		global g
--		g = Tkinter.StringVar()
-+		g = tkinter.StringVar()
- 		self.g_seq = Entry(master, bd=5, textvariable=g).grid(row=1,column=5)
- 		
- 		self.label = Label(master, text="Path to -h").grid(row=1,column=6)		
- 		global h
--		h = Tkinter.StringVar()
-+		h = tkinter.StringVar()
- 		self.h_seq = Entry(master, bd=5, textvariable=h).grid(row=1,column=7)
- 		
- 		self.label = Label(master, text="Path to -i").grid(row=2,column=0)		
- 		global i
--		i = Tkinter.StringVar()
-+		i = tkinter.StringVar()
- 		self.i_seq = Entry(master, bd=5, textvariable=i).grid(row=2,column=1)
- 		
- 		self.label = Label(master, text="Path to -j").grid(row=2,column=2)		
- 		global j
--		j = Tkinter.StringVar()
-+		j = tkinter.StringVar()
- 		self.j_seq = Entry(master, bd=5, textvariable=j).grid(row=2,column=3)
- 		
- 		self.label = Label(master, text="Path to -k").grid(row=2,column=4)		
- 		global k
--		k = Tkinter.StringVar()
-+		k = tkinter.StringVar()
- 		self.k_seq = Entry(master, bd=5, textvariable=k).grid(row=2,column=5)
- 		
- 		self.label = Label(master, text="Path to -l").grid(row=2,column=6)		
- 		global l
--		l = Tkinter.StringVar()
-+		l = tkinter.StringVar()
- 		self.l_seq = Entry(master, bd=5, textvariable=l).grid(row=2,column=7)
- 		
- 		self.label = Label(master, text="Path to -m").grid(row=3,column=0)		
- 		global m
--		m = Tkinter.StringVar()
-+		m = tkinter.StringVar()
- 		self.m_seq = Entry(master, bd=5, textvariable=m).grid(row=3,column=1)
- 		
- 		self.label = Label(master, text="Path to -n").grid(row=3,column=2)		
- 		global n
--		n = Tkinter.StringVar()
-+		n = tkinter.StringVar()
- 		self.n_seq = Entry(master, bd=5, textvariable=n).grid(row=3,column=3)
- 		
- 		self.label = Label(master, text="Path to -o").grid(row=3,column=4)		
- 		global o
--		o = Tkinter.StringVar()
-+		o = tkinter.StringVar()
- 		self.o_seq = Entry(master, bd=5, textvariable=o).grid(row=3,column=5)
- 		
- 		self.label = Label(master, text="Path to -p").grid(row=3,column=6)		
- 		global p
--		p = Tkinter.StringVar()
-+		p = tkinter.StringVar()
- 		self.p_seq = Entry(master, bd=5, textvariable=p).grid(row=3,column=7)
- 		
- 		self.label = Label(master, text="Path to -q").grid(row=4,column=0)		
- 		global q
--		q = Tkinter.StringVar()
-+		q = tkinter.StringVar()
- 		self.q_seq = Entry(master, bd=5, textvariable=q).grid(row=4,column=1)
- 		
- 		self.label = Label(master, text="Path to -r").grid(row=4,column=2)		
- 		global r
--		r = Tkinter.StringVar()
-+		r = tkinter.StringVar()
- 		self.r_seq = Entry(master, bd=5, textvariable=r).grid(row=4,column=3)
- 		
- 		self.label = Label(master, text="Path to -s").grid(row=4,column=4)		
- 		global s
--		s = Tkinter.StringVar()
-+		s = tkinter.StringVar()
- 		self.s_seq = Entry(master, bd=5, textvariable=s).grid(row=4,column=5)
- 		
- 		self.label = Label(master, text="Path to -t").grid(row=4,column=6)		
- 		global t
--		t = Tkinter.StringVar()
-+		t = tkinter.StringVar()
- 		self.t_seq = Entry(master, bd=5, textvariable=t).grid(row=4,column=7)
- 		
- 		self.label = Label(master, text="Path to -u").grid(row=5,column=0)		
- 		global u
--		u = Tkinter.StringVar()
-+		u = tkinter.StringVar()
- 		self.u_seq = Entry(master, bd=5, textvariable=u).grid(row=5,column=1)
- 		
- 		self.label = Label(master, text="Path to -v").grid(row=5,column=2)		
- 		global v
--		v = Tkinter.StringVar()
-+		v = tkinter.StringVar()
- 		self.v_seq = Entry(master, bd=5, textvariable=v).grid(row=5,column=3)
- 		
- 		self.label = Label(master, text="Path to -w").grid(row=5,column=4)		
- 		global w
--		w = Tkinter.StringVar()
-+		w = tkinter.StringVar()
- 		self.w_seq = Entry(master, bd=5, textvariable=w).grid(row=5,column=5)
- 		
- 		self.label = Label(master, text="Path to -x").grid(row=5,column=6)		
- 		global x
--		x = Tkinter.StringVar()
-+		x = tkinter.StringVar()
- 		self.x_seq = Entry(master, bd=5, textvariable=x).grid(row=5,column=7)
- 		
- 		self.label = Label(master, text="Path to -y").grid(row=6,column=0)		
- 		global y
--		y = Tkinter.StringVar()
-+		y = tkinter.StringVar()
- 		self.y_seq = Entry(master, bd=5, textvariable=y).grid(row=6,column=1)
- 		
- 		self.label = Label(master, text="Path to -z").grid(row=6,column=2)		
- 		global z
--		z = Tkinter.StringVar()
-+		z = tkinter.StringVar()
- 		self.z_seq = Entry(master, bd=5, textvariable=z).grid(row=6,column=3)
- 		"""
- 		self.label = Label(master, text="Path to -n")
-@@ -648,19 +648,19 @@
- 				cmd += " -o " + o.get()
- 		os.system(cmd)
- 	def h(self):
--		print "========================================================="
--		print "This is GUI for PHYX designed to make input easier"
--		print "Type the location of the file or value into the box"
--		print "For help on a program, type anything into the help box"
--		print "and click the program you want help with. Not all options are"
--		print "needed for all programs so only fill in boxes used for "
--		print "the program of interest. Anything extra filled in will be" 
--		print "ignored if it is not an option for the program"
--		print "If the programs option does not require an argument"
--		print "simply type something into the box and it will activate"
--		print "that argument"
--		print "Copyright (C) 2015 FePhyFoFum\nLicense GPLv3\nwritten by Joseph F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim)"
--		print "========================================================="
-+		print("=========================================================")
-+		print("This is GUI for PHYX designed to make input easier")
-+		print("Type the location of the file or value into the box")
-+		print("For help on a program, type anything into the help box")
-+		print("and click the program you want help with. Not all options are")
-+		print("needed for all programs so only fill in boxes used for ")
-+		print("the program of interest. Anything extra filled in will be") 
-+		print("ignored if it is not an option for the program")
-+		print("If the programs option does not require an argument")
-+		print("simply type something into the box and it will activate")
-+		print("that argument")
-+		print("Copyright (C) 2015 FePhyFoFum\nLicense GPLv3\nwritten by Joseph F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim)")
-+		print("=========================================================")
- 
- 
- root = Tk()

debian/patches/series

-2to3.patch
 link_lnlopt.patch

debian/rules

@@ -16,8 +16,14 @@ endif
 override_dh_auto_install:
 	mkdir -p $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin
 	dh_auto_install -- prefix=$(CURDIR)/debian/$(DEB_SOURCE)/usr
-	echo "#!/usr/bin/python3" > $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/Phyx_Gui
-	cat src/Phyx_Gui.py >> $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/Phyx_Gui
+	#echo "#!/usr/bin/python3" > $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/Phyx_Gui
+	#cat src/Phyx_Gui.py >> $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/Phyx_Gui
 
 override_dh_compress:
 	dh_compress --exclude=.pdf
+
+override_dh_auto_clean:
+	rm -rf src/phyx.logfile
+	if [ -r src/Makefile ]; then \
+	  $(MAKE) -C src distclean; \
+	fi

src/Phyx_Gui.py

-import Tkinter,os,sys
-from Tkinter import *
-
-
-class GUI:
-	def __init__(self, master):
-		
-		self.master = master
-		master.title("PHYX GUI")
-		
-		self.label = Label(master, text="Path to -a").grid(row=0,column=0)
-		#self.label.pack()
-		
-		global a
-		a = Tkinter.StringVar()
-		self.a_seq = Entry(master, bd=5, textvariable=a).grid(row=0,column=1)
-		#self.aa_seq.pack(side = LEFT)
-
-		self.label = Label(master, text="Path to -b").grid(row=0,column=2)
-		#self.label.pack(side = LEFT)
-
-		global b
-		b = Tkinter.StringVar()
-		self.b_seq = Entry(master, bd=5, textvariable=b).grid(row=0,column=3)
-		#self.b_seq.pack(side = LEFT)
-		
-		self.label = Label(master, text="Path to -c").grid(row=0,column=4)
-		#self.label.pack(side = LEFT)
-		
-		global c
-		c = Tkinter.StringVar()
-		self.c_seq = Entry(master, bd=5, textvariable=c).grid(row=0,column=5)
-		#self.c_seq.pack(side = LEFT)
-		
-		self.label = Label(master, text="Path to -d").grid(row=0,column=6)
-		#self.label.pack(side = LEFT)
-		
-		global d
-		d = Tkinter.StringVar()
-		self.d_seq = Entry(master, bd=5, textvariable=d).grid(row=0,column=7)
-		#self.d_seq.pack(side = LEFT)
-		
-		self.label = Label(master, text="Path to -e").grid(row=1,column=0)		
-		global e
-		e = Tkinter.StringVar()
-		self.e_seq = Entry(master, bd=5, textvariable=e).grid(row=1,column=1)
-		
-		self.label = Label(master, text="Path to -f").grid(row=1,column=2)		
-		global f
-		f = Tkinter.StringVar()
-		self.f_seq = Entry(master, bd=5, textvariable=f).grid(row=1,column=3)
-		
-		self.label = Label(master, text="Path to -g").grid(row=1,column=4)		
-		global g
-		g = Tkinter.StringVar()
-		self.g_seq = Entry(master, bd=5, textvariable=g).grid(row=1,column=5)
-		
-		self.label = Label(master, text="Path to -h").grid(row=1,column=6)		
-		global h
-		h = Tkinter.StringVar()
-		self.h_seq = Entry(master, bd=5, textvariable=h).grid(row=1,column=7)
-		
-		self.label = Label(master, text="Path to -i").grid(row=2,column=0)		
-		global i
-		i = Tkinter.StringVar()
-		self.i_seq = Entry(master, bd=5, textvariable=i).grid(row=2,column=1)
-		
-		self.label = Label(master, text="Path to -j").grid(row=2,column=2)		
-		global j
-		j = Tkinter.StringVar()
-		self.j_seq = Entry(master, bd=5, textvariable=j).grid(row=2,column=3)
-		
-		self.label = Label(master, text="Path to -k").grid(row=2,column=4)		
-		global k
-		k = Tkinter.StringVar()
-		self.k_seq = Entry(master, bd=5, textvariable=k).grid(row=2,column=5)
-		
-		self.label = Label(master, text="Path to -l").grid(row=2,column=6)		
-		global l
-		l = Tkinter.StringVar()
-		self.l_seq = Entry(master, bd=5, textvariable=l).grid(row=2,column=7)
-		
-		self.label = Label(master, text="Path to -m").grid(row=3,column=0)		
-		global m
-		m = Tkinter.StringVar()
-		self.m_seq = Entry(master, bd=5, textvariable=m).grid(row=3,column=1)
-		
-		self.label = Label(master, text="Path to -n").grid(row=3,column=2)		
-		global n
-		n = Tkinter.StringVar()
-		self.n_seq = Entry(master, bd=5, textvariable=n).grid(row=3,column=3)
-		
-		self.label = Label(master, text="Path to -o").grid(row=3,column=4)		
-		global o
-		o = Tkinter.StringVar()
-		self.o_seq = Entry(master, bd=5, textvariable=o).grid(row=3,column=5)
-		
-		self.label = Label(master, text="Path to -p").grid(row=3,column=6)		
-		global p
-		p = Tkinter.StringVar()
-		self.p_seq = Entry(master, bd=5, textvariable=p).grid(row=3,column=7)
-		
-		self.label = Label(master, text="Path to -q").grid(row=4,column=0)		
-		global q
-		q = Tkinter.StringVar()
-		self.q_seq = Entry(master, bd=5, textvariable=q).grid(row=4,column=1)
-		
-		self.label = Label(master, text="Path to -r").grid(row=4,column=2)		
-		global r
-		r = Tkinter.StringVar()
-		self.r_seq = Entry(master, bd=5, textvariable=r).grid(row=4,column=3)
-		
-		self.label = Label(master, text="Path to -s").grid(row=4,column=4)		
-		global s
-		s = Tkinter.StringVar()
-		self.s_seq = Entry(master, bd=5, textvariable=s).grid(row=4,column=5)
-		
-		self.label = Label(master, text="Path to -t").grid(row=4,column=6)		
-		global t
-		t = Tkinter.StringVar()
-		self.t_seq = Entry(master, bd=5, textvariable=t).grid(row=4,column=7)
-		
-		self.label = Label(master, text="Path to -u").grid(row=5,column=0)		
-		global u
-		u = Tkinter.StringVar()
-		self.u_seq = Entry(master, bd=5, textvariable=u).grid(row=5,column=1)
-		
-		self.label = Label(master, text="Path to -v").grid(row=5,column=2)		
-		global v
-		v = Tkinter.StringVar()
-		self.v_seq = Entry(master, bd=5, textvariable=v).grid(row=5,column=3)
-		
-		self.label = Label(master, text="Path to -w").grid(row=5,column=4)		
-		global w
-		w = Tkinter.StringVar()
-		self.w_seq = Entry(master, bd=5, textvariable=w).grid(row=5,column=5)
-		
-		self.label = Label(master, text="Path to -x").grid(row=5,column=6)		
-		global x
-		x = Tkinter.StringVar()
-		self.x_seq = Entry(master, bd=5, textvariable=x).grid(row=5,column=7)
-		
-		self.label = Label(master, text="Path to -y").grid(row=6,column=0)		
-		global y
-		y = Tkinter.StringVar()
-		self.y_seq = Entry(master, bd=5, textvariable=y).grid(row=6,column=1)
-		
-		self.label = Label(master, text="Path to -z").grid(row=6,column=2)		
-		global z
-		z = Tkinter.StringVar()
-		self.z_seq = Entry(master, bd=5, textvariable=z).grid(row=6,column=3)
-		"""
-		self.label = Label(master, text="Path to -n")
-		self.label.pack(padx=10)
-		
-		global test2
-		test2 = Tkinter.StringVar()
-		self.nuc_seq = Entry(master, bd=5, textvariable=test2)
-		self.nuc_seq.pack(padx=10)
-		
-		self.label = Label(master, text="Outfile -o")
-		self.label.pack()
-		
-		global test3
-		test3 = ""
-		test3 = Tkinter.StringVar()
-		self.out_seq = Entry(master, bd=5, textvariable=test3)
-		self.out_seq.pack()
-		
-		self.label = Label(master, text="help -h")
-		self.label.pack()
-		
-		global help_me
-		help_me = ""
-		help_me = Tkinter.StringVar()
-		self.help_seq = Entry(master, bd=5, textvariable=help_me)
-		self.help_seq.pack()
-		"""
-		self.aa_button = Button(master, text="Run pxaatocdn", command=self.aa).grid(row=7,column=0)
-		#self.aa_button.pack()
-		
-		self.bdfit_button = Button(master, text="Run pxbdfit", command=self.bdfit).grid(row=7,column=1)
-		
-		self.bdsim_button = Button(master, text="Run pxbdsim", command=self.bdsim).grid(row=7,column=2)
-		
-		self.boot_button = Button(master, text="Run pxboot", command=self.boot).grid(row=7,column=3)
-		
-		self.bp_button = Button(master, text="Run pxbp", command=self.bp).grid(row=7,column=4)
-		
-		self.bpseq_button = Button(master, text="Run pxbpseq", command=self.bpseq).grid(row=7,column=5)
-
-		self.cat_button = Button(master, text="Run pxcat", command=self.cat).grid(row=7,column=6)
-
-		self.clsq_button = Button(master, text="Run pxclsq", command=self.clsq).grid(row=7,column=7)
-
-		self.conseq_button = Button(master, text="Run pxconseq", command=self.conseq).grid(row=8,column=0)
-
-		self.contrates_button = Button(master, text="Run pxcontrates", command=self.contrates).grid(row=8,column=1)
-
-		self.fqfilt_button = Button(master, text="Run pxfqfilt", command=self.fqfilt).grid(row=8,column=2)
-
-		self.lsseq_button = Button(master, text="Run pxlsseq", command=self.lsseq).grid(row=8,column=3)
-
-		self.lstr_button = Button(master, text="Run pxlstr", command=self.lstr).grid(row=8,column=4)
-		
-		self.mrca_button = Button(master, text="Run pxmrca", command=self.mrca).grid(row=8,column=5)
-
-		self.mrcacut_button = Button(master, text="Run pxmrcacut", command=self.mrcacut).grid(row=8,column=6)
-
-		self.mrcaname_button = Button(master, text="Run pxmrcaname", command=self.mrcaname).grid(row=8,column=7)
-
-		self.nj_button = Button(master, text="Run pxnj", command=self.nj).grid(row=9,column=0)
-
-		self.nni_button = Button(master, text="Run pxnni", command=self.nni).grid(row=9,column=1)
-
-		self.nw_button = Button(master, text="Run pxnw", command=self.nw).grid(row=9,column=2)
-
-		self.recode_button = Button(master, text="Run pxrecode", command=self.recode).grid(row=9,column=3)
-
-		self.revcomp_button = Button(master, text="Run pxrevcomp", command=self.revcomp).grid(row=9,column=4)
-
-		self.rms_button = Button(master, text="Run pxrms", command=self.rms).grid(row=9,column=5)
-
-		self.rmt_button = Button(master, text="Run pxrmt", command=self.rmt).grid(row=9,column=6)
-
-		self.rr_button = Button(master, text="Run pxrr", command=self.rr).grid(row=9,column=7)
-
-		self.seqgen_button = Button(master, text="Run pxseqgen", command=self.seqgen).grid(row=10,column=0)
-
-		self.stofa_button = Button(master, text="Run pxstofa", command=self.stofa).grid(row=10,column=1)
-
-		self.stonex_button = Button(master, text="Run pxstonex", command=self.stonex).grid(row=10,column=2)
-
-		self.stophy_button = Button(master, text="Run pxstophy", command=self.stophy).grid(row=10,column=3)
-
-		self.strec_button = Button(master, text="Run pxstrec", command=self.strec).grid(row=10,column=4)
-
-		self.sw_button = Button(master, text="Run pxsw", command=self.sw).grid(row=10,column=5)
-
-		self.tlate_button = Button(master, text="Run pxtlate", command=self.tlate).grid(row=10,column=6)
-
-		self.upgma_button = Button(master, text="Run pxupgma", command=self.upgma).grid(row=10,column=7)
-
-		#self.seqgen_button.pack()
-		
-		self.h_button = Button(master, text="print help menu", command=self.h).grid(row=11,column=3)
-		#self.h_button.pack()
-		#global help_on
-		#help_on = ""
-		#help_on = Tkinter.StringVar()
-		
-		self.close_button = Button(master, text="Close program", command=master.quit).grid(row=11,column=4)
-		#self.close_button.pack()
-	def aa(self):
-		if (h.get() != ""):
-			cmd = "pxaatocdn -h"
-		else: 
-			cmd = "pxaatocdn -a " + a.get() + " -n " + n.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def bdfit(self):
-		if (h.get() != ""):
-			cmd = "pxbdfit -h"
-		else: 
-			cmd = "pxbdfit -t " + t.get()
-			if (m.get() != ""):
-				cmd += " -m " + m.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def bdsim(self):
-		if (h.get() != ""):
-			cmd = "pxbdsim -h"
-		else: 
-			cmd = "pxbdsim "
-			if (e.get() != ""):
-				cmd += " -e " + e.get()
-			if (t.get() != ""):
-				cmd += " -t " + t.get()
-			if (b.get() != ""):
-				cmd += " -b " + b.get()
-			if (d.get() != ""):
-				cmd += " -d " + d.get()
-			if (n.get() != ""):
-				cmd += " -n " + n.get()
-			if (s.get() != ""):
-				cmd += " -s " + s.get()
-			if (x.get() != ""):
-				cmd += " -x " + x.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def boot(self):
-		if (h.get() != ""):
-			cmd = "pxboot -h"
-		else: 
-			cmd = "pxboot "
-			if (s.get() != ""):
-				cmd += " -s " + s.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-			if (p.get() != ""):
-				cmd += " -p " + p.get()
-			if (f.get() != ""):
-				cmd += " -f " + f.get()
-			if (x.get() != ""):
-				cmd += " -x " + x.get()
-		os.system(cmd)
-	def bp(self):
-		if (h.get() != ""):
-			cmd = "pxbp -h"
-		else: 
-			cmd = "pxbp -t" + t.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def bpseq(self):
-		if (h.get() != ""):
-			cmd = "pxbpseq -h"
-		else: 
-			cmd = "pxbpseq -t" + t.get() + " -s " + s.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def cat(self):
-		if (h.get() != ""):
-			cmd = "pxcat -h"
-		else: 
-			cmd = "pxcat -s " + s.get()
-			if (p.get() != ""):
-				cmd += " -p " + p.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def clsq(self):
-		if (h.get() != ""):
-			cmd = "pxclsq -h"
-		else: 
-			cmd = "pxclsq -s " + s.get()
-			if (p.get() != ""):
-				cmd += " -p " + p.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def conseq(self):
-		if (h.get() != ""):
-			cmd = "pxconseq -h"
-		else: 
-			cmd = "pxconseq -s " + s.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def contrates(self):
-		if (h.get() != ""):
-			cmd = "pxcontrates -h"
-		else: 
-			cmd = "pxcontrates -s " + s.get()
-			if (c.get() != ""):
-				cmd += " -c " + c.get()
-			if (t.get() != ""):
-				cmd += " -t " + t.get()
-			if (a.get() != ""):
-				cmd += " -a " + a.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def fqfilt(self):
-		if (h.get() != ""):
-			cmd = "pxfqfilt -h"
-		else: 
-			cmd = "pxfqfilt -s " + s.get()
-			if (m.get() != ""):
-				cmd += " -m " + m.get()
-			if (s.get() != ""):
-				cmd += " -s " + s.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def lsseq(self):
-		if (h.get() != ""):
-			cmd = "pxlsseq -h"
-		else: 
-			cmd = "pxlsseq -s " + s.get()
-			if (a.get() != ""):
-				cmd += " -a "
-			if (p.get() != ""):
-				cmd += " -p "
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def lstr(self):
-		if (h.get() != ""):
-			cmd = "pxlstr -h"
-		else: 
-			cmd = "pxlstr -t " + t.get()
-			if (a.get() != ""):
-				cmd += " -a "
-			if (r.get() != ""):
-				cmd += " -r "
-			if (b.get() != ""):
-				cmd += " -b "
-			if (u.get() != ""):
-				cmd += " -u "
-			if (n.get() != ""):
-				cmd += " -n "
-			if (l.get() != ""):
-				cmd += " -l "
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def mrca(self):
-		if (h.get() != ""):
-			cmd = "pxmrca -h"
-		else: 
-			cmd = "pxmrca -t " + t.get()
-			if (m.get() != ""):
-				cmd += " -m " + m.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def mrcacut(self):
-		if (h.get() != ""):
-			cmd = "pxmrcacut -h"
-		else: 
-			cmd = "pxmrcacut -t " + t.get()
-			if (m.get() != ""):
-				cmd += " -m " + m.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def mrcaname(self):
-		if (h.get() != ""):
-			cmd = "pxmrcaname -h"
-		else: 
-			cmd = "pxmrcaname -t " + t.get()
-			if (m.get() != ""):
-				cmd += " -m " + m.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def nj(self):
-		if (h.get() != ""):
-			cmd = "pxnj -h"
-		else: 
-			cmd = "pxnj -s " + s.get()
-			if (n.get() != ""):
-				cmd += " -n " + n.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def nni(self):
-		if (h.get() != ""):
-			cmd = "pxnni -h"
-		else: 
-			cmd = "pxnni -t " + t.get()
-			if (x.get() != ""):
-				cmd += " -x " + x.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def nw(self):
-		if (h.get() != ""):
-			cmd = "pxnw -h"
-		else: 
-			cmd = "pxnw -s " + s.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-			if (a.get() != ""):
-				cmd += " -a " + a.get()
-			if (t.get() != ""):
-				cmd += " -t " + t.get()
-			if (m.get() != ""):
-				cmd += " -m " + m.get()
-			if (n.get() != ""):
-				cmd += " -n " + n.get()
-			if (v.get() != ""):
-				cmd += " -v " + v.get()
-		os.system(cmd)
-	def recode(self):
-		if (h.get() != ""):
-			cmd = "pxrecode -h"
-		else: 
-			cmd = "pxrecode -s " + s.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def revcomp(self):
-		if (h.get() != ""):
-			cmd = "pxrevcomp -h"
-		else: 
-			cmd = "pxrevcomp -s " + s.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def rms(self):
-		if (h.get() != ""):
-			cmd = "pxrms -h"
-		else: 
-			cmd = "pxrms -s " + s.get()
-			if (r.get() != ""):
-				cmd += " -r " + r.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def rmt(self):
-		if (h.get() != ""):
-			cmd = "pxrmt -h"
-		else: 
-			cmd = "pxrmt -t " + t.get()
-			if (n.get() != ""):
-				cmd += " -n " + n.get()
-			if (f.get() != ""):
-				cmd += " -f " + f.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def rr(self):
-		if (h.get() != ""):
-			cmd = "pxrr -h"
-		else: 
-			cmd = "pxrr -t " + t.get()
-			if (f.get() != ""):
-				cmd += " -f " + f.get()
-			if (u.get() != ""):
-				cmd += " -u " + u.get()
-			if (s.get() != ""):
-				cmd += " -s " + s.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def seqgen(self):
-		if (h.get() != ""):
-			cmd = "pxseqgen -h"
-		else: 
-			cmd = "pxseqgen -t " + t.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-			if (l.get() != ""):
-				cmd += " -l " + l.get()
-			if (c.get() != ""):
-				cmd += " -c "
-			if (b.get() != ""):
-				cmd += " -b " + b.get()
-			if (w.get() != ""):
-				cmd += " -w " + w.get()
-			if (q.get() != ""):
-				cmd += " -q " + q.get()
-			if (g.get() != ""):
-				cmd += " -g " + g.get()
-			if (r.get() != ""):
-				cmd += " -r " + r.get()
-			if (n.get() != ""):
-				cmd += " -n " + n.get()
-			if (x.get() != ""):
-				cmd += " -x " + x.get()
-			if (a.get() != ""):
-				cmd += " -a "
-			if (p.get() != ""):
-				cmd += " -p "
-			if (m.get() != ""):
-				cmd += " -m " + m.get()
-			if (k.get() != ""):
-				cmd += " -k " + k.get()
-		os.system(cmd)
-	def stofa(self):
-		if (h.get() != ""):
-			cmd = "pxstofa -h"
-		else: 
-			cmd = "pxstofa -s " + s.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def stonex(self):
-		if (h.get() != ""):
-			cmd = "pxstonex -h"
-		else: 
-			cmd = "pxstonex -s " + s.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def stophy(self):
-		if (h.get() != ""):
-			cmd = "pxstophy -h"
-		else: 
-			cmd = "pxstophy -s " + s.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def strec(self):
-		if (h.get() != ""):
-			cmd = "pxstrec -h"
-		else: 
-			cmd = "pxstrec -d" + d.get()
-			if (w.get() != ""):
-				cmd += " -w "
-			if (z.get() != ""):
-				cmd += " -z "
-			if (t.get() != ""):
-				cmd += " -t " + t.get()
-			if (c.get() != ""):
-				cmd += " -c " + c.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-			if (n.get() != ""):
-				cmd += " -n " + n.get()
-			if (a.get() != ""):
-				cmd += " -a " + a.get()
-			if (m.get() != ""):
-				cmd += " -m " + m.get()
-			if (p.get() != ""):
-				cmd += " -p " + p.get()
-			if (l.get() != ""):
-				cmd += " -l " + l.get()
-		os.system(cmd)
-	def sw(self):
-		if (h.get() != ""):
-			cmd = "pxsw -h"
-		else: 
-			cmd = "pxsw -s" + s.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-			if (a.get() != ""):
-				cmd += " -a " + a.get()
-			if (t.get() != ""):
-				cmd += " -t " + t.get()
-			if (m.get() != ""):
-				cmd += " -m " + m.get()
-			if (n.get() != ""):
-				cmd += " -n " + n.get()
-			if (v.get() != ""):
-				cmd += " -v " + v.get()
-		os.system(cmd)
-	def tlate(self):
-		if (h.get() != ""):
-			cmd = "pxtlate -h"
-		else: 
-			cmd = "pxtlate -s " + s.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def upgma(self):
-		if (h.get() != ""):
-			cmd = "pxupgma -h"
-		else: 
-			cmd = "pxupgma -s " + s.get()
-			if (o.get() != ""):
-				cmd += " -o " + o.get()
-		os.system(cmd)
-	def h(self):
-		print "========================================================="
-		print "This is GUI for PHYX designed to make input easier"
-		print "Type the location of the file or value into the box"
-		print "For help on a program, type anything into the help box"
-		print "and click the program you want help with. Not all options are"
-		print "needed for all programs so only fill in boxes used for "
-		print "the program of interest. Anything extra filled in will be" 
-		print "ignored if it is not an option for the program"
-		print "If the programs option does not require an argument"
-		print "simply type something into the box and it will activate"
-		print "that argument"
-		print "Copyright (C) 2015 FePhyFoFum\nLicense GPLv3\nwritten by Joseph F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim)"
-		print "========================================================="
-
-
-root = Tk()
-my_gui = GUI(root)
-root.mainloop()